Genomic paradigms for food-borne enteric pathogen analysis at the USFDA: case studies highlighting method utility, integration and resolution

• Published in: Food additives & contaminants. Part A, Chemistry, analysis, control, exposure & risk assessment Vol. 30; no. 8; pp. 1422 - 1436
• Main Authors: Elkins, C.A, Kotewicz, M.L, Jackson, S.A, Lacher, D.W, Abu-Ali, G.S, Patel, I.R
• Format: Journal Article Conference Proceeding
• Language: English
• Published: Abingdon Taylor & Francis 01.08.2013; Taylor & Francis Ltd
• Subjects: Animals; Bacteria; Biological and medical sciences; Biotechnology; case studies; Center for Food Safety and Applied Nutrition; chromosome mapping; Deoxyribonucleic acid; Disease Outbreaks; DNA; DNA, Bacterial - genetics; Escherichia coli; Food industries; food pathogens; Food safety; food-borne bacterial pathogens; Foodborne Diseases - epidemiology; Foodborne Diseases - microbiology; Fundamental and applied biological sciences. Psychology; genes; Genome, Bacterial; genomic methods; Genomics; Genomics - methods; Genotype; Genotype & phenotype; genotyping; Government agencies; Humans; microarray technology; monitoring; Oligonucleotide Array Sequence Analysis; Phylogeny; regulatory science; risk reduction; Salmonella enterica; Salmonella enterica - genetics; serotypes; Shiga toxin-producing Escherichia coli; Shiga-Toxigenic Escherichia coli - genetics; single nucleotide polymorphism; strain discrimination; United States - epidemiology; United States Food and Drug Administration; United States; United States > US; regulatory science; Genomics; Method; Strain; Case study; Regulation(control); Discrimination; Analysis; Pathogenic; genomic methods; strain discrimination; Bacteria; food-borne bacterial pathogens; Food
• ISSN: 1944-0057; 1944-0049; 1944-0057
• DOI: 10.1080/19440049.2012.743192

Modern risk control and food safety practices involving food-borne bacterial pathogens are benefiting from new genomic technologies for rapid, yet highly specific, strain characterisations. Within the United States Food and Drug Administration (USFDA) Center for Food Safety and Applied Nutrition (CFSAN), optical genome mapping and DNA microarray genotyping have been used for several years to quickly assess genomic architecture and gene content, respectively, for outbreak strain subtyping and to enhance retrospective trace-back analyses. The application and relative utility of each method varies with outbreak scenario and the suspect pathogen, with comparative analytical power enhanced by database scale and depth. Integration of these two technologies allows high-resolution scrutiny of the genomic landscapes of enteric food-borne pathogens with notable examples including Shiga toxin-producing Escherichia coli (STEC) and Salmonella enterica serovars from a variety of food commodities. Moreover, the recent application of whole genome sequencing technologies to food-borne pathogen outbreaks and surveillance has enhanced resolution to the single nucleotide scale. This new wealth of sequence data will support more refined next-generation custom microarray designs, targeted re-sequencing and “genomic signature recognition” approaches involving a combination of genes and single nucleotide polymorphism detection to distil strain-specific fingerprinting to a minimised scale. This paper examines the utility of microarrays and optical mapping in analysing outbreaks, reviews best practices and the limits of these technologies for pathogen differentiation, and it considers future integration with whole genome sequencing efforts.